Calculation Parameters

miRanda algorithm used by metaRNA accepts the following optional parameters.

Parameter Type Default Description
scale float 4.0 The 5’ miRNA scaling parameter.
strict int 0 Perform a Strict Seed search when set to 1.
gap_open float -9.0 Gap-open Penalty
gap_extend float -4.0 Gap-extend Penalty
score_threshold float 50.0 Score Threshold for reporting hits
energy_threshold float 1.0 Energy Threshold for reporting hits
length_5p_for_weighting int 8 The 5’ sequence length to be weighed except for the last residue.
temperature int 30 Used while calculating Free Energy
alignment_len_threshold int 8 Minimum alignment.

Passing Parameters

The parameters are passed as keyword arguments.

targets = scan(gene_sequence, mirna_sequence, scale=5.0, strict=1)